Question: R - GEOQuery getting abandoned ?
1
gravatar for lindfors.erno
4.3 years ago by
Germany
lindfors.erno20 wrote:

Hi all,

I understand from a discussion 3 years back (Bioconductor: Package "Is Not Available") R 2.13 (or so) is the latest R version that is compatible with GEOQuery package.

Does anybody know if there are plans to update this package to fresher R versions?

Or could it be so this package is getting abandoned?
From what I understand the purpose of this package is to encapsulate R's weak formatting and parsing features but since nowadays R is being integrated quite well with high-level programming language (e.g. http://rforge.net/Rserve/), so the formatting and parsing can be smoothly be done with a high-level programming language.

Thanks,
Erno Lindfors

geoquery R • 1.7k views
ADD COMMENTlink modified 2.2 years ago by Biostar ♦♦ 20 • written 4.3 years ago by lindfors.erno20
1

I should add that the purpose of the package has nothing to do with some weakness in R. The purpose of the package is to allow querying the GEO database remotely and fetching datasets from it. R is a high level programming language and Rserve would have nothing to do with this (it enables R to act as a server by responding to requests over TCP/IP).

ADD REPLYlink written 4.3 years ago by Devon Ryan90k
3
gravatar for Sean Davis
4.3 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

Please refer to the official Bioconductor for packages as the primary source of information regarding availability and installation instructions:

http://bioconductor.org/packages/release/bioc/html/GEOquery.html

Note that if you follow the installation instructions, you will get the most recent version of GEOquery available for your version of R.  GEOquery is and will continue to be supported.

ADD COMMENTlink written 4.3 years ago by Sean Davis25k
1

Thanks, recently managed to get GEOquery working!

When sending my original message GEOquery was not installed properly in my computer and I was getting an error message that gave an impression GEOquery is not compatible with the R version I am  using.

To get GEOquery installed properly the main trick was that it requires the libxml2 and libcurl4 development packages in Ubuntu as brought up in There were no GEOquery function after installing .
It might be reasonable to include something about this in the installation instructions of GEOquery.

Glad to hear GEOquery is compatible with most recent R versions!

ADD REPLYlink written 4.3 years ago by lindfors.erno20
1

GEOquery requires the RCurl and XML packages and the libcurl4 and libxml2 requirements are from those packages, not GEOquery directly.  You will have received error messages for RCurl and XML.

ADD REPLYlink written 4.3 years ago by Sean Davis25k
2
gravatar for Devon Ryan
4.3 years ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

You misread that thread. GEOquery is fully supported by the most recent versions of R and I've heard no news of that changing in the foreseeable future. The problem in that thread was misspelling the package name. It's GEOquery, not GEOQuery. Just for reference:

> library(GEOquery)
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] GEOquery_2.32.0     Biobase_2.26.0      BiocGenerics_0.12.1

loaded via a namespace (and not attached):
[1] bitops_1.0-6   RCurl_1.95-4.5 XML_3.98-1.1  
ADD COMMENTlink written 4.3 years ago by Devon Ryan90k
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